chr4-125891418-A-G

Variant names:

• chr4-125891418-A-G
• rs1506169
• ENST00000667497.1:n.164-124899A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667497.1(ENSG00000250149):​n.164-124899A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,958 control chromosomes in the GnomAD database, including 3,247 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (3247 hom., cov: 31)
• Consequence: ENSG00000250149 ENST00000667497.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 0 publications found

Genes affected

ENSG00000250149 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250149	ENST00000667497.1	n.164-124899A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28525 AN: 151842 Hom.: 3242 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.186

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.188 AC: 28547 AN: 151958 Hom.: 3247 Cov.: 31 AF XY: 0.193 AC XY: 14319 AN XY: 74238

African (AFR) AF: 0.122 AC: 5059 AN: 41470

American (AMR) AF: 0.302 AC: 4600 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 649 AN: 3468

East Asian (EAS) AF: 0.451 AC: 2314 AN: 5136

South Asian (SAS) AF: 0.318 AC: 1534 AN: 4818

European-Finnish (FIN) AF: 0.214 AC: 2261 AN: 10554

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11596 AN: 67974

Other (OTH) AF: 0.192 AC: 407 AN: 2116

Alfa AF: 0.179 Hom.: 8809

Bravo AF: 0.192

Asia WGS AF: 0.428 AC: 1486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.53
PhyloP100		-0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1506169; hg19: chr4-126812573;